From 7d88c7ef1928585557101e771fb078e4a93baa90 Mon Sep 17 00:00:00 2001 From: Elizabeth Partan Date: Wed, 8 Apr 2026 10:54:00 -0400 Subject: [PATCH] Update norm_integration.qmd Harmony creates a PCA-like layer (so do not re-run PCA after Harmony before running UMAP) --- 02_integration/norm_integration.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/02_integration/norm_integration.qmd b/02_integration/norm_integration.qmd index 84c7b6d..eac869e 100644 --- a/02_integration/norm_integration.qmd +++ b/02_integration/norm_integration.qmd @@ -582,6 +582,7 @@ seurat_harmony <- readRDS("seurat_harmony.rds") #| eval: !expr "!exists('seurat_harmony')" #| warning: false #| message: false +# IntegrateLayers creates a PCA-like layer (so do not re-run PCA below before running UMAP) ## Here seurat will integrate on the level of sample id. If you want to integrate on other aspects the SCT normalization will need to be done with all of the data together. # seurat_sctnorm[["RNA"]] <- split(seurat_sctnorm[["RNA"]], f = seurat_sctnorm$orig.ident) seurat_harmony <- IntegrateLayers( @@ -591,7 +592,6 @@ seurat_harmony <- IntegrateLayers( new.reduction = "harmony", assay = "SCT", verbose = FALSE ) -seurat_harmony <- RunPCA(seurat_harmony) seurat_harmony <- RunUMAP(seurat_harmony, reduction = "harmony", dims = 1:40,